The present invention relates to a portable biochip scanner device used to detect and acquire fluorescence signal data from biological microchips (biochips), in particular oligonucleotide biochips.
A related U.S. Pat. No. 6,329,661, entitled xe2x80x9cA BIOCHIP SCANNER DEVICExe2x80x9d, by Alexander Perov, Alexander I. Belgovskiy and Andrei D. Mirzabekov is being filed on the same day as the present patent application.
At the present time, biochips, after being incubated with a sample solution containing fluorescently labeled target molecules are assayed using either a microscope equipped with a charge coupled device (CCD) camera or a laser scanner. To acquire large volume of digital data (1-100 MB per image) in a reasonable time these devices employ sophisticated optical, mechanical, and electronic components which results in high cost of the hardware used. Regardless of the technique of fluorescence measurement used, all known biochip analyzers are high-resolution imaging instruments. This means that their output data is essentially a digital image of the chip composed of approximately 1000N elementary data points, where N represents the number of biochip immobilization sites. As a biochip user is typically interested in relative fluorescence intensities of the immobilization sites, an image as the output data format is highly redundant and requires further processing before the data can be analyzed. This may include signal integration over the immobilization sites, background subtraction, and normalization. The image processing is especially difficult in the case of analyzers based on wide-field microscopes, in which both the sensitivity and the image background are inherently non-uniform. With increasing complexity of biochips, the software for processing the fluorescence data becomes increasing intricate and rather demanding in terms of computer memory and processor speed.
The above identified related application discloses a novel technique of reading biochips that we refer to as Discrete Scanning (or Row Scanning) and a laser scanner that embodies this principle in practice. In contrast to the imaging scanners, this device scans exclusively the rows of a biochip array, the beam focal spot being adjusted to match the size of the array elements. The scanner employs a HeNe laser emitting at 594 nm to excite Texas Red-labeled target molecules, an optical system with a fiber-optic output for delivery of the excitation light to a miniature scanning head, and a low-noise photodiode as a fluorescence detector. A computer-controlled positioning system is used to move the scanning head in both X and Y directions to monitor the intensity of fluorescence for each element of a 2D biochip array. The-above setup provides a detection threshold and dynamic range close to those of commercially available biochip readers. In the same time, it is much less demanding in terms of the amplifiers bandwidth, analog-to-digital conversion rate, optical resolution, and scanning mechanics parameters.
There is, however, a need for even simpler and portable biochip reader device. These requirements are typical for applications in which the number of biochip array elements sufficient to assure adequate analytical capability is relatively small, for example, a few hundred or even less.
A principal object of the present invention is to provide a portable biochip scanner device used to detect and acquire fluorescence signal data from biological microchips (biochips) and method of use. Other important objects of the present invention are to provide such method and portable biochip scanner device substantially without sacrificing the sensitivity and dynamic range; and to overcome some disadvantages of prior art arrangements.
In brief, a portable biochip scanner device used to detect and acquire fluorescence signal data from biological microchips (biochips) is provided. The portable biochip scanner device employs a laser for emitting an excitation beam. An optical fiber delivers the laser beam to a portable biochip scanner. A lens collimates the laser beam, the collimated laser beam is deflected by a dichroic mirror and focused by an objective lens onto a biochip. The fluorescence light from the biochip is collected and collimated by the objective lens. The fluorescence light is delivered to a photomultiplier tube (PMT) via an emission filter and a focusing lens. The focusing lens focuses the fluorescence light into a pinhole. A signal output of the PMT is processed and displayed.